Copernicus marine data

[MarkusKonk]

@Marie59
There seems to be a compatibility issue. Or is there something wrong with my cmd?
copernicusmarine subset --dataset-id "med-cmcc-tem-rean-d" --variable "thetao" --minimum-latitude "38.42" --maximum-latitude "43.60" --minimum-longitude "-0.46" --maximum-longitude "6.1728" --minimum-depth "0.0" --maximum-depth "3000" --start-datetime "2022-01-01" --end-datetime "2022-01-03"

[bgruening]

There is a new conda package available with major new version 2.3.3. Maybe we need to bump the client here?

[MarkusKonk]

I could make a PR, but I don't know how to test it locally...

[bgruening]

Maybe @Marie59 can test your PR?

[MarkusKonk]

I would actually be curious how to test it locally because I need to develop a very similar tool for AquaInfra anyway (which is why I checked this one). Is there some documentation or a guide?

[yvanlebras]

Hi Markus! Live from Bogota (and with colleagues of you if I am not saying mistakes ;) ) it appears to me the error message can be linked to an update of CMEMS service side, maybe updating as proposed by Björn it can be ok @Marie59 ? This issue also make me rethink about an existing tool who can used credentials from marine copernicus but the good manner to manage such credentials was not ready on the Galayx side, it seems to me this is the case now so we can also maybe consider updating this medenv tool ?

[bgruening]

@MarkusKonk if you are fine with the fact that you need Galaxy 25.1 (not release, but branched), then we have this feature included: galaxyproject/galaxy#19084

We put one year of work into a framework to handle better credentials for tools. And we would appreciate if you can develop your tool with this new framework. I will also encourage @Marie59 and @yvanlebras to migrate old tools to this new secret infrastructure.

[MarkusKonk]

@bgruening Looks good and when I add the credentials to the XML, the tool asks me to create the corresponding credentials group. However, I get the following error when I try to do so:

I added vault_config_file: vault_conf.yml to the galaxy.yml.sample file but still get the error.

@yvanlebras Yes, send my regards to Merret and Vanessa :)

[MarkusKonk]

Oh wait, I just saw the vault.md. I will go through this first.

[bgruening]

I think you need to fill out / configure the vault_conf.yml see https://docs.galaxyproject.org/en/latest/admin/special_topics/vault.html

also ping @arash77 for better ideas.

[arash77]

The way I chose to configure the vault_conf.yml is using the database method, which only requires a random key.

[MarkusKonk]

That worked, thanks!

[Marie59]

Hi all ! Sorry I arrive a bit after everything ... can I help on anything ? (I'll be more available by thursday next week)

ping @jeromedetoc

[yvanlebras]

Hi @MarkusKonk , @Marie59 , if I am not wrong, we can close as all work on updating the copernicus oriented tools credentials have fiwed the issue isn't it?

[Marie59]

Yes normally, now it should all work fine ;)